Child of the TARDIS
by TheSovereigntyofReality
Summary: Fresh out of the Time War, the Doctor finds the escaped Melody Pond. This is the beginning of a timey-whimey wibbly-wobbly event. Includes a few old friends. Doctor/River Amy/Rory. I only own Dani and associated characters and concepts
1. The Girl

**New York, USA, 1969**

The Doctor ran through the streets. His ship was prodding him along with an urgency that startled him. He'd never known her to be quite so scared of any one thing. Now she pushed him towards something. So he ran.

He was honestly surprised he was still alive. He'd ended the war and spent eight months curled up in a ball or hiding inside his own head. He couldn't sleep now. He kept hearing the screams…smelling the planet burn…feeling the pain that led up to his regeneration. His TARDIS was all the Doctor had left of his home.

He turned into an alley and slowed to a stop. There was a human child slumped against the wall, pale and slightly blue. And the TARDIS was pushing him towards her. The Doctor walked over, pulling off his jacket, and crouched next to her. He wrapped her up and lifted her.

'What's the interest in you then?' he asked the unconscious child.

**Florida**

A Presan hybrid walked through the orphanage with a cardboard box. She packed away first photographs and then all the toys. As a child in the orphanage, this particular little girl didn't have many toys. The hybrid lifted her head as an ugly woman with an eyepatch stepped in behind her.

'Where's the girl?' she demanded.

'Why would I tell you that?' the hybrid asked, inspecting the bedside lamp. 'You kidnapped her. I'm hardly going to help you do it again, am I? Especially considering who I am.'

'Who are you?' the hag snapped. 'Another one of the Doctor's strays?'

The hybrid dropped the last of the child's belongings into the box and turned around.

'You could say that.' She threw herself back into the glass window and through.

As she went down she flipped in mid-air. It was a two story drop and she landed on her feet, unharmed. Then she shot off. She knew what was going on in New York and she also knew there were things the Doctor had to know now. Timelines had to be preserved, after all.

**New York**

Since the TARDIS had sent him out after her, the Doctor took her back there. He took her straight to the infirmary. He looked her over as he grabbed the computer and activated the scan. She was bruised, dirty and her eyelids were flickering, brow furrowed, as if she was having nightmares.

The computer beeped and the Doctor looked at the readings. His jaw dropped slightly and then he looked over his shoulder. A scowl was on his face as he looked at the ship wall,

'This is not funny!'

A roll of annoyance told him it wasn't a joke. The TARDIS was serious. He stared at the readings. This little girl had two hearts, a self-renewing cell structure and respiratory bypass. But, if she was Gallifreyan, why couldn't he sense her? Why was she affected by the cold of Earth? What was she doing on Earth in the first place?

'Run a species analysis,' he said.

He waited for the results of that. The beam ran over her and the figures beeped onto the screen: HUMAN-TIME LORD HYBRID. The Doctor squinted at it. It explained why she was on Earth. She was born here, but how did she get Time Lord DNA? She was – what? – seven?

The Doctor's attention was diverted when a square popped up at the corner of the screen and it showed a dark-haired girl with slightly Asian features walking towards the TARDIS with a box in her hands. And she seemed aware of the fact that it wasn't a normal blue box.

The Doctor picked the small girl up and carried her out of the infirmary. The older girl could just wait outside. He had to take care of this kid first. He took her across the room and smiled when he saw the TARDIS had already set up a room for her. The Doctor laid her on the bed and tucked her in.

Then he walked down and headed out, through the console room. When he opened the door, the girl was waiting there, the box sitting at her feet. Up closer, the Doctor saw that she reminded him of someone. He closed the door behind him and faced her, crossing his arms over his chest.

'Who are you?' he asked.

'Zaphire,' the girl answered. 'Zaphire Singe. I'm half-Presan and I just came from 2027.'

She held up her vortex manipulator. The Doctor nodded as his mind filled in the blanks. If she was from 2027, it was about the right time for her to be Dani's daughter. And that was who she reminded him of.

'So you came about that kid I picked up?' the Doctor asked.

'Yeah,' Zaphire nodded. 'I grew up with her. She's my best friend. Of course, that's still to come for her.'

_Guess I'll be taking a trip to see Dani, then. _The Doctor looked down at the box again. And then he looked up at Zaphire. She appeared to be deep in thought. She was hopefully working out what she could and couldn't tell him.

'How is she half-human, half-Gallifreyan?' the Doctor asked.

'That's a long story,' Zaphire said.

The Doctor opened the door and let her in.

Zaphire carried the box into the TARDIS console room. It was different from how she knew it to be. Seemed smaller. Zaphire put the box on the floor near the console. Then she went over and sat in the pilot's seat. The Doctor walked around the console, asking,

'So how's this long story go?'

'You'll have to forgive me for leaving chunks out,' Zaphire said. 'Timelines, you understand?'

'Go on, then.'


	2. Melody

'Her name's Melody,' Zaphire explained. 'Due to circumstances surrounding her conception, she was born with Time Lord DNA. It was just "human plus" back then. That's why they chose her. All she really had was regeneration and maybe two hearts.'

'Who are "they"?' the Doctor asked.

'They think of themselves as a religious order.' Zaphire scoffed. '_We_ call them a cult. They don't have any Gods or deities to speak of. Just one single, stupid belief. They think that when the oldest question in the universe is asked, silence will fall.'

'What's the question?' the Doctor asked.

'I have got my suspicions,' Zaphire said. 'They think you're the only one with the answer, so they want to kill you before you can give it. What do they do? They kidnap a child with Time Lord DNA, amp said DNA up until she's a hybrid and turn her into a weapon whose sole purpose is to bring you down.'

The Doctor pressed his lips together. Melody had probably run away from whoever this lot were. If they thought he was going to sit back and let them do this to an innocent little girl, they had another think coming. But…

'You said you grew up with her.'

'I did,' Zaphire laughed. 'In 2010, mum opened a school in London for aliens called the Kaias Boarding School. I started in 2014 and you brought Melody to us in 2015. That's why I brought her stuff.'

'Sounds reasonable,' the Doctor walked over to the lever and threw it.

The column moved and the TARDIS was thrown into the Time Vortex. The Doctor walked around to the console monitor and looked at the readings. Then he looked back up at Zaphire.

'How did they get their hands on Melody?' he asked.

'She was travelling with you at the time,' Zaphire answered. 'They replaced her with a flesh avatar that melted upon discovery. But there were little clues that she wasn't the original article. Unexplainable pains, an inconclusive pregnancy test. My mum met the avatar once. She said it smelt too fresh, but back then mum assumed it was just a perfume she was wearing.'

'But how did they catch her?' the Doctor asked.

Zaphire stood up and started circling in the console. For a moment, she seemed to collect her thoughts. The only reason the Doctor waited for her was because she was Dani's daughter. She seemed to be just like her.

'For a long time, we didn't know, but I think I do now,' she answered. 'When I went into that room, that I'm sure Melody's mum also went into, the dresser had all these photos over the top of it. All photos of Melody. And one photo showed her as a baby, with her mum holding her. I presume she came in then and these guys followed her in. Her mum must've realised that Melody was her daughter.'

'No mother would run away while her child needed her,' the Doctor murmured.

'Double for if the mother in question had travelled with you,' Zaphire agreed.

They both looked over as they heard soft footfalls. A moment later, Melody peeked out from the passage. The Doctor smiled and knelt down so he was at her level, even from that distance.

'Hello,' he said.

She blinked and then tentatively stepped into the console room. The Doctor could see that she was nervous around anyone. It was probably due to the treatment her captors had given her, but he and Dani could show her the love that she'd been deprived of for so long. And so would Zaphire.

She stopped just outside of arms length of the Doctor. He smiled in what he hoped was a reassuring way – he had no idea, seeing as he had no clue how he looked – and held his hand out for her. She stared at it for a moment before she reached out and took his hand. He gently pulled her into his arms and lifted her.

'You all right, then?' he asked.

She nodded.

'Who are you?' she asked.

'I'm a friend,' he told her. 'I'm going to take you somewhere safe, where the people that hurt you can't get to you.'

Melody smiled and rested her head on his shoulder,

'Thank you.'

**London, England, 2015**

Dani looked over at her seven-year-old daughter.

She was taking Melody out to show her their dorm room and she was carrying the box. Dani looked at the Doctor. He'd told her everything that Zaphire would tell him in twelve years. Dani sat back behind her desk.

'I assume you don't want her to know who saved her until the damage is undone?' Dani asked. 'Or, as much as possible.'

'She would have been taught I'm evil,' the Doctor explained. 'I don't want to panic her.'

'Half-human, half-Time Lady,' Dani shook her head. 'The next time you see her, you won't recognise her. I heard the story. You've still got to live it.'

'Hm.' The Doctor nodded.

Dani pulled her feet down.

'Two things,' she said. 'This whole ordeal doesn't actually start until you're in your eleventh life, so ignore it for now.'

'Two?' the Doctor asked.

'The Nestine Consciousness is attacking the Earth.' Dani checked a sticky note on her desk. 'In late March, 2005. They've got a relay device in the roof of the central city Hendricks's. You look about right to do that. It was an interesting couple of days. And you'll meet Zaph's dad. Although, I wasn't thinking anywhere along those lines back then.'

'Looking forward to it,' the Doctor said. 'I'll just drop your adult daughter to her appropriate time and I'll see you then.'

He walked into the TARDIS. Dani smiled and watched it vanish. She then hit the intercom and said,

'Could you send the Chesterton Professors up here, please?'


	3. River Song

**Demon's Run, 52nd Century**

It dawned on the Doctor and he didn't know how he could've been so blind. Melody Pond; River Song. It was obvious, really. He didn't know why he hadn't noticed before. His mind flashed back to that terrified little girl. _Melody. _Of course he'd realised it was the baby as soon as he realised Amy had given birth to the Child of the TARDIS.

'Hello.' That was all he could think to say.

'Hello.' She smiled at him.

He smiled,

'But that means…!' _She's the daughter of Amy and Rory._

'I'm afraid it does.' She nodded.

'Oh!' The Doctor pointed. 'You and I, we…we…we…uh…'

He made kissing gestures. River leaned forward,

'Yessss.'

'Oh!' He clapped his hands together. Then he glanced back at Amy and Rory. They were watching him in confusion. He turned back to River, stretched his arms out and adjusted his appearance. He had things to do and he had already done all he could for her. 'How do I look?'

'Amazing,' she told him.

'I better be.' He pointed to her again.

'Yes, you better be.'

The Doctor turned around,

'Amy, Rory. I know where your daughter is and, on my life, she will be safe. Vashta, Jenny, 'til next time. River, get them all home.' He ran towards the TARDIS and soniced it, taking the force-field off.

Amy and Rory ran after him, calling for him. He ducked into the TARDIS, but he had to duck out again. He had to look at her again. He pointed to her for the third time, delighted.

'You…!'

He ducked inside again. River would tell them and Amy and Rory would know that their little girl would be safe. In the meantime, the Doctor had to fill in some blanks.

But this was brilliant!

No wonder Zaph hadn't been able to say much! And it had made the universe more bearable knowing there was another one of his kind, no matter how unintentional it was. He was the Last Pure Time Lord, but he only ever told a grand total of four people that: Dani, Rose, Jack and Sarah. To everyone else, he was the Last of the Time Lords.

He'd known, even then, that anyone who couldn't shut up could jeopardise that little girl. Martha and Donna hadn't been told because, good as they were, they had the tendency to shoot their mouths off.

The thought of who he'd told about this reminded him of something. He pulled the lever.

**London, England, 2015**

Dani was finishing the final paperwork for Melody's admittance when she heard it again.

She looked up as the TARDIS materialised. The door opened and a Doctor with floppy brown hair, a large jaw and a bow tie walked out. Dani assumed what was going on here.

'Eleventh?' she asked.

'Yeah,' he said. 'Melody was just kidnapped in my timestream. She's the daughter of my companions, Amy and Rory.'

'Where and when are they from?' Dani asked.

'Leadworth, four years ago,' the Doctor answered. 'Donna told you about River Song?'

'The woman that died for you in the Library?' Dani asked. 'She came up, yeah.'

'That's who Melody is.'

'Oh.' Dani leaned back in the chair. 'Wow. Okay, I picked a last name off the top of my head and she's listed as "Melody Zucker". Should I change it?'

'No,' the Doctor said. 'These people won't give up.'

'What happened, Doctor?'

**Cardiff, Wales, 2002**

Jack Harkness looked up from the files as he heard the distinctive sound of the TARDIS materialising. He walked into the lounge room and he grinned when he saw the Doctor walk out with a new body. He looked around and grinned when he saw Jack.

'Captain,' he said. 'What year is this?'

'2002,' Jack answered.

'Oh!' the Doctor groaned. 'Too early. Oh, well. I suppose it doesn't matter. I am aware that you want an explanation for your inability to die, but I'm afraid it'll have to wait. I explained it to you when I was in my last life.'

'Nice to know,' Jack said. 'So what are you doing here?'

'Do you remember when I told you about that half-human, half-Time Lady child that I found?' the Doctor asked. 'The one the cult wanted to kill me with?'

'Yeah,' Jack agreed. 'What about her?'

'She was just born in my timeline,' the Doctor answered. 'She got the Time Lord DNA because she was conceived on board the TARDIS. I probably shouldn't have taken Amy and Rory on a trip on their wedding night.'

Jack grinned.

'Ooo!' he exclaimed. 'Fun!'

'Not really,' the Doctor answered. 'She's just been kidnapped. Now, I can't do anything for her beyond what I've already done two lifetimes ago. But what do you know of a certain Dr. River Song?'

'River Song? She's an archaeologist that's been convicted of murder and sentenced to twelve consecutive life sentences. She's in Stormcage but she comes and goes as she pleases. Everyone in the Time Agency heard of her.' Jack's eyes widened. 'She's not Melody, is she?'

The Doctor nodded.

'How did that happen?' Jack asked.

**London, England, 2010**

Sarah Jane Smith turned around as she heard the sound of the TARDIS. K-9's ears started rotating and he reported,

'Time distortion, mistress.'

Sarah Jane stood up and watched the TARDIS materialise. Once it was solid, the door opened and the Doctor stepped out. When she'd seen him last, he'd saved Luke from getting hit by a car. She'd known he was regenerating and now she saw what he had regenerated into.

'How did it happen this time?' Sarah Jane asked, gesturing to his body. 'I didn't have the chance to ask.'

'Same way it happened the first time you saw the regeneration,' the Doctor answered. 'What's the date, Sarah?'

'June, 18th, 2010,' Sarah Jane said. 'The kids are all in school.'

'All right.' The Doctor looked around. 'Sarah, remember when I told you about Melody?'

'The little girl that's half-human, half-Time Lady?' Sarah Jane asked. 'The one who that cult was trying to mould into a weapon to kill you?'

'That's her,' the Doctor agreed. 'It's finally happened in my timestream. I know the full story now. The cult in question is called the Silence. They've been manipulating and killing the people of Earth for billions of year.'

'But even UNIT doesn't know about them,' Sarah Jane pointed out. 'Why not?'

'Because when you look away from them, you forget you ever saw them in the first place,' the Doctor answered. 'So, I used that against them. I put footage on the recording of Neil Armstrong's moon landing so the human race drives them out themselves. And I saw Melody when she was in their hands. I recognised her. They'd stuffed her into a mechanicalised spacesuit and they used her to kidnap her mother. She was terrified.'

Sarah Jane could see the anger in the Doctor. If she thought he was angry when he initially told her, it was nothing compared to now. Now he understood why. He knew the parents and he knew the girl.

'What happened, Doctor?' Sarah Jane asked.


	4. River's Life

**Cell 426, Stormcage Containment Facility, 5145**

River Song looked up as she heard the sound of the TARDIS. She stepped forward and opened the gate, ensuring to do it just right so the alarms didn't go off. When it was solid, the Doctor stepped out. She could tell something bad had just happened. She'd know that look anywhere. He wore that expression when he let someone down. The Doctor walked towards her slowly, almost apprehensively. He right stopped on the threshold of the cell door. His hand came up and cupped her face. She reached up and caught his hand, stoking his knuckles with her thumb.

'Where are we?' she asked softly.

'I just did Demon's Run.'

'Oh, sweetie.' She leaned up and kissed him. He returned the kiss harder than he usually kissed her outside of lovemaking. She broke the kiss when he sobbed against her mouth. She pressed her forehead against his. 'It's all right, my love.'

'I lost you,' he whispered. 'I let them take you.'

'And you found me,' she argued softly. 'You took me somewhere safe. You saved me.'

'Dani saved you,' he breathed. 'Zaph saved you. The TARDIS saved you. The only reason I found you is because the TARDIS did. She pushed me to you. Then Zaph showed up and told me what needed to happen. Dani taught you to be a living being.'

She took his hand and led him into the TARDIS. He followed her and, as she passed the console, he flicked the lever and sent them into the vortex. She guided him into the south passage and into the lounge room. Then she pushed him down into the couch and sat in his lap. His arms clamped around her waist and he buried his face in her neck. She felt his tears on her skin and stroked his hair.

'Hush now, love,' she gentled him. 'It's all right now. I'm fine.'

'You weren't,' he whispered hoarsely. 'You were hurt. You almost froze to death.'

'But I didn't,' River murmured. 'You did save me.'

'Tell me about it?' he quietly requested. 'Tell me about your life in the school.'

'Dani, Morge and Zaph lived there, so during holidays, I'd stay with them,' River told him. 'Mum and dad would come to spend the holidays with us. In 2011, Jack went and told them what had happened and where I was. They knew if I was taken out of the school before I was ready, the Silence would get me again. With my arrival, Dani started looking for everything she could find on the Silence. She started improving the barriers so that a person's genetic code has to be uploaded to the Kaias Foundation's computer core before they can enter by any means.'

'That ought to do it,' the Doctor breathed.

'When I was fourteen, though, I had to regenerate.'

The Doctor lifted his head and looked at her.

'Why?' he asked.

'They got their hands on a Kaias graduate,' River answered. 'He wouldn't tell them anything though. One of our classes is "Survival Lying". Exactly what it says on the box: we learn to lie convincingly to survive on Earth. They tortured him to see if I was there, but he wouldn't answer. So they extracted it from his brain.'

'Was he all right?' the Doctor asked.

'They dumped him on Earth, hoping to lure the protectors out.' River smirked. 'It was 2023. They didn't realise the school's protections were not alive. They didn't tell us, of course. Zaph and I were at that age where you think you're invincible and you disobey the adults because you think you don't need them.'

'You snuck out of the school,' the Doctor stated.

She nodded,

'I was shot between the hearts. I'm just glad I went with Zaph. Anyone else and they would've caught me again. She carried me back in before I regenerated. Only then did Dani tell everyone what had happened. I overheard her apologising to my parents in a way I am certain she learned from you through observation. Mum and dad told me off and by that I mean, mum guilt-tripped me and dad told me off. "Have you got any idea what will happen if they catch you again"; "it was just luck last time when the Doctor found you". It was true, I grant. And later mum came in and told me she understood how I felt. I have a free spirit but I had to remain within the walls of one building.'

'What did Dani do about the Silence?' the Doctor asked.

'Honestly, she copped out,' River answered. 'I don't know why. Maybe she couldn't afford to just blow them up herself at the time or maybe she was just feeling petulant.'

'What did she do?' the Doctor asked.

'She called the Time Agency.'

The Doctor paused,

'Did she stick her tongue out at them as they were taken away?'

'No,' River answered. 'She turned her back on them and walked back to the school.'

'It was the first one.' The Doctor dropped his head on River's shoulder again. 'Dani always sticks her tongue out when she's being petulant.'


	5. The Kaias Boarding School

**Leadworth, England, 2011**

Rory came back. He didn't look happy either. Amy could guess, even without him saying it. At the same time, he looked confused.

'The clerics are outside,' he said. 'But they're getting beaten up by somebody.'

'Good,' Amy said.

There doorbell rang and she and Rory looked at each other. Amy grabbed the vase on the table next to the couch as she went to answer the door. If it was someone hostile, she wanted a weapon. If not, she didn't want to look paranoid. She opened the door and…

'Jack?' she exclaimed. 'Jack Harkness?'

'Hi, Amy,' he said. 'The Kaias Foundation are just keeping the clerics busy while I come in and deliver a message. Hi, Rory.'

'What message?' Rory asked. 'Come on in, Jack.'

'It's a message from the Doctor,' Jack said, stepping inside and Amy closed the door behind him. 'I used to travel with him a long time ago.'

'Is it Melody?' Amy asked. 'Did he find her?'

'Two regenerations ago,' Jack answered. 'I used to be a Time Agent. Then the Agency swiped two years of my memories and I became a conman. That's how I met the Doctor. Can we sit down for this?'

Amy and Rory sat on the couch and Jack sat in the chair.

'He'd just come out of the Time War,' Jack said. 'You've heard of it?'

Amy and Rory both nodded. Jack continued,

'The TARDIS tracked her down and prodded him to her. She was freezing to death in an alley. The Doctor didn't know who she was back then, but he knew she was important if the TARDIS had her as a priority. So he took her back to the ship. First he scanned her to see what kind of damage she had. That was when Zaphire, the girl that'll be your daughter's best friend, showed up. She'd come from 2027, gotten Melody's things and come to tell the Doctor what needed to happen.'

'Which is?' Rory asked. 'I doubt he can bring her home. The clerics and the Silence are hanging around Leadworth waiting for that, aren't they?'

'I'm afraid so.' Jack winced apologetically. 'The Doctor came to me in 2002 to explain this to me. The Kaias Foundation is a defence force made up almost entirely of aliens and it was organised by the Doctor's old ward, Dani. She's also Zaph's mother. Last year, she set up the Kaias Boarding School in the middle of London.'

'Is it where the Doctor took our baby?' Amy asked.

'Yes,' Jack said. 'In four years. Dani will develop one of the greatest defences I've ever heard of. You won't be able to enter the school unless your genetic code is loaded into the data bank. She'll send someone to get you once the Doctor tells her in 2015 and he went to her before he came to me.'

'Is that was you came here all those years ago?' Amy asked. 'To ensure Melody was born. I mean, I thought my husband was gay and you proved me wrong.'

Rory grinned at the memory. That had been a very strange time and he hadn't understood Jack's interest back then. Now he did.

'Actually, I had no idea on that,' Jack laughed. 'I came here to familiarise you with me so I could tell you this quickly. I just didn't want to risk a paradox that would stop Melody ever being born.'

'And thank you for that,' Rory said. He frowned. 'Did the Doctor find out any more about the Silence? Why did they take our daughter?'

'He only knows what Zaphire told him,' Jack answered. 'They're a cult. They consider themselves a religious order, though. They believe that when the oldest question in the universe is answered, silence will fall. Hence the name. They also believe the Doctor is the only one who knows the answer to the question, so they want him dead before he can answer it.'

'Do you know what the question is?' Amy asked.

'No.' Jack frowned. 'But I suspect it's the question that everybody he meets asks him.'

Amy and Rory both knew which question Jack was talking about. They glanced at each other. Then Amy said it,

'Doctor Who?'


End file.
